The company that wants to licence a super trawler to fish in Australian waters has vowed to fight any ban on its operations.

The Senate has passed legislation stopping the super trawler Abel Tasman operating for up to two years.

Environment Minister Tony Burke says he now has the legal powers to make sure that Australia is not taking risks with the ocean.

"My priority is to make sure that we look after the environment. This Government's made some very strong decisions when it comes to protection of our oceans," he said.

"I am determined that we don't have other decisions that undo that."

Mr Burke expects to be able to use the new laws as early as tomorrow.

He says Seafish Tasmania will have two weeks to comment on the legislation, then he and the Fisheries Minister will set up a new expert panel.

"If the extra checks I need to be done are done, and they come back with a complete clean bill of health...then we'll back the science in."

"But I can't have a situation where I'm expected to rush to decisions when that answer that comes back is...the research isn't done, the science is really old."

Legal options

The Abel Tasman, formerly the Margiris, was brought to Australia as part of a joint venture between Seafish Tasmania, which has a fishing quota of almost 18,000 tonnes, and a Dutch company.

Seafish Tasmania director Gerry Geen says the company will pursue all legal and other options to fight the laws on the the basis of discrimination.

"If the Government thinks we'll just walk away, they are wrong," he said in a statement.

"We understand there are a number of legal and other avenues still open to us, including the option of going fishing.

"We believe strongly that, in addition to the discriminatory nature of the Minister's intervention with legislation at the last possible moment, there have also been unfair administrative and procedural delays in a number of government agencies over the past few weeks.

Destructive or sustainable?

The size of the Margiris, now named Abel Tasman, has sparked fears it will decimate fish stocks.

But Australia's fishing regulator says the trawler's quota is based on sound science.

So will the super trawler devastate a region, or will its catch be a drop in the ocean?

"Additionally we've also been denied natural justice by the Ombudsman's office, the one agency that is supposed to protect the rights of individuals against bureaucratic maladministration, which produced its interim findings without even talking to us."

Mr Geen says the vessel is still at Port Lincoln in South Australia and will remain there until there is greater certainty about its future.

"Unfortunately we're unable to retain all the Tasmanians we employed for this venture and have had to let them go," he said.

"Should we eventually be permitted to go fishing, we will seek to re-employ them."

The Environment Minister says he is not sure what to make of Mr Geens' claims of discrimination.

"There is an impact on people who are going to have an impact on the environment," Mr Burke said.

"That is what the environmental law is there to do.

"To use words such as what is in that media release, really ignores the fact that national environmental law is there for a purpose.

"In terms of the clauses that I am intending to activate tomorrow, they are new parts of environmental law and companies were not in a position to be able to deal with that until they came into the environmental law.

No case

A constitutional law expert believes Seafish Tasmania has little chance of compensation.

George Williams from the University of New South Wales has told ABC Local Radio the Commonwealth frequently changes laws affecting individual rights, but it does not automatically give rise to compensation.

"It's very hard to see they've got any particularly strong chances," he said.

"That's because the federal law has been drafted specifically to stymie their attempt to fish and when you've got a specific federal law that is dealing with this case in a way that very clearly gives the minister new, very broad powers, it's hard to see you can do anything about that."

Prof. Williams says the Government may choose to grant compensation.

"I think increasing the political risk for a government is probably much more likely."

"Perhaps if the government is concerned that there is damage to Australia's national interest, particularly if this becomes a big issue overseas and as investors start thinking again about coming to Australia, or perhaps there might be embarassment because of correspondence, then that sort of discretionary factor might come into play."

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